Is the ladder to the upper Habitat open to the rover bay? What about planets without an atmosphere, or poisonous/corrosive atmospheres? Will we suffocate in bed?

The ladder hatch and the upper area is indeed open to the rover bay, meaning if you open the doors it will vent all the living quarters. This as an intentional design decision. The ship is designed for operations down to planets with breathable atmospheres with the crew compartment there to make the crew comfortable if they have to wait for troops to return. Obviously, if you are away and dropping into a dangerous atmosphere, you can suit up in advance to prevent injury.